chrX-71189260-G-A

Variant names:

• chrX-71189260-G-A
• rs5981086
• ENST00000450860.1:n.268-5243C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000450860.1(ENSG00000228427):​n.268-5243C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 110,271 control chromosomes in the GnomAD database, including 1,197 homozygotes. There are 4,183 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.14 (1197 hom., 4183 hem., cov: 21)
• Consequence: ENSG00000228427 ENST00000450860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891
• Publications: 1 publications found

Genes affected

ENSG00000228427 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985688	XR_001755878.2	n.286-5243C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228427	ENST00000450860.1	n.268-5243C>T		intron_variant	Intron 1 of 1	3
ENSG00000228427	ENST00000652147.3	n.358-5247C>T		intron_variant	Intron 1 of 1
ENSG00000228427	ENST00000664514.4	n.600-5243C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 15178 AN: 110218 Hom.: 1192 Cov.: 21

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0909

Gnomad SAS AF: 0.0570

Gnomad FIN AF: 0.0840

Gnomad MID AF: 0.0979

Gnomad NFE AF: 0.0719

Gnomad OTH AF: 0.116

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.138 AC: 15194 AN: 110271 Hom.: 1197 Cov.: 21 AF XY: 0.128 AC XY: 4183 AN XY: 32615

African (AFR) AF: 0.288 AC: 8722 AN: 30267

American (AMR) AF: 0.105 AC: 1089 AN: 10331

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 371 AN: 2624

East Asian (EAS) AF: 0.0911 AC: 311 AN: 3412

South Asian (SAS) AF: 0.0549 AC: 142 AN: 2586

European-Finnish (FIN) AF: 0.0840 AC: 494 AN: 5879

Middle Eastern (MID) AF: 0.0981 AC: 21 AN: 214

European-Non Finnish (NFE) AF: 0.0719 AC: 3795 AN: 52783

Other (OTH) AF: 0.120 AC: 180 AN: 1501

Alfa AF: 0.107 Hom.: 583

Bravo AF: 0.148

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.55
DANN	Benign	0.68
PhyloP100		-0.89

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs5981086; hg19: chrX-70409110;